Re: [Jmol-users] loading a string from my database in the JmolApplet

Bob Hanson Sat, 20 Nov 2004 19:18:11 -0800

I agree with Miguel -- this isn't the approach. Why don't you describe what you are after here, and let us help you determine what code will work. I think in this case what you are doing is inserting the molecule from the database and trying to avoid use of separate molecule files, right? If so, then the best thing to do is avoid using jmol.js in this case and just create the applet tag yourself using the <param name=LoadInline> tag.

But, Miguel, am I right that this is still broken in 10pre17? I just noticed that myself at http://www.stolaf.edu/people/hansonr/jmol/inline I remember you switched to "inline" instead of "loadinline" for the parameter name for 10pre11 - 10pre16, but you were going to switch back, I think, to "loadInline" right? But I don't see that working. Something is broken there.

I'll have to see how the Gaussian files are being parsed. I notice that now my "fake" Gaussian format for loadInline doesn't work any longer as well. Hmm. That's my problem, not yours, of course.

But the <param name=LoadInline> needs to get fixed or at least better specified.

Bob

fr wrote:

Hi and thanks for the tips.
I tried it but with no success. Others things seem to be on fire.
For the moment, I save my string coordonates in a file and I read the file
as before to load it the applet. Not too slow but a bit tricky ...
Hope will be soon repare.
Bye and thanks for this very nice software.
FR
-----Message d'origine-----
De : [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] la part de Bob Hanson
Envoye : samedi 20 novembre 2004 01:45
A : [EMAIL PROTECTED]
Objet : Re: [Jmol-users] loading a string from my database in the
JmolApplet
What you need is some JavaScript that does the following:
(provided 10pre17 works)
 molecule="|"+molecule.replace(/\|/g,"")
 molecule=molecule.replace(/\r\n/g,"|")
 molecule=molecule.replace(/\n/g,"|")
 molecule=molecule.replace(/\r/g,"|")
 molecule=molecule.replace(/\|/g,"\n|")
This corrects for different browser endline issues.
fr chalaoux wrote:
Hi All,
I tried  to load a string from my database in the JmolApplet .
The probleme is that the applet is loaded but apparently not the
molecule in the applet.
Any idea ?
Bye, FR.
Code with jmol10 pre17
===================
<html>
 <head>
   <title>nitrogens</title>
   <script src="../jmol/Jmol.js"></script> 
<script language="JavaScript">
    function init() {
     var molecule;
     molecule = document.TheForm.amol.value;
     jmolLoadInline(molecule);
     }
</script>
 </head>
<body onload="init()">
<form name="TheForm">
<input type="text" name="amol" value="REMARK  FINAL COORDINATES WRITTEN
BY NAMD AT TIMESTEP 1000
ATOM      1  C1  LIG     1       0.708  -1.202   0.152  0.00
0.00      LIG
ATOM 2 C2 LIG 1 0.813 0.302 0.452 0.00
0.00      LIG
ATOM 3 C3 LIG 1 -0.563 1.002 0.405 0.00
0.00      LIG
ATOM 4 C4 LIG 1 -1.701 0.128 -0.154 0.00
0.00      LIG
ATOM 5 N1 LIG 1 -0.382 -1.824 0.907 0.00
0.00      LIG
ATOM 6 C5 LIG 1 -1.695 -1.256 0.535 0.00
0.00      LIG
ATOM 7 C6 LIG 1 1.856 1.000 -0.438 0.00
0.00      LIG
ATOM 8 N2 LIG 1 3.228 0.639 -0.038 0.00
0.00      LIG
ATOM 9 C7 LIG 1 4.000 -0.096 -1.050 0.00
0.00      LIG
ATOM 10 C8 LIG 1 3.989 1.762 0.529 0.00
0.00      LIG
ATOM 11 N3 LIG 1 -3.014 0.806 -0.023 0.00
0.00      LIG
ATOM 12 C9 LIG 1 -3.053 2.184 -0.548 0.00
0.00      LIG
ATOM 13 C10 LIG 1 -4.206 0.065 -0.483 0.00
0.00      LIG
ATOM 14 C11 LIG 1 -0.365 -3.289 0.762 0.00
0.00      LIG
ATOM 15 F1 LIG 1 -4.439 -1.057 0.271 0.00
0.00      LIG
ATOM 16 H1 LIG 1 0.561 -1.398 -0.913 0.00
0.00      LIG
ATOM 17 H2 LIG 1 1.638 -1.691 0.444 0.00
0.00      LIG
ATOM 18 H3 LIG 1 1.166 0.408 1.480 0.00
0.00      LIG
ATOM 19 H4 LIG 1 -0.479 1.919 -0.177 0.00
0.00      LIG
ATOM 20 H5 LIG 1 -0.836 1.321 1.413 0.00
0.00      LIG
ATOM 21 H6 LIG 1 -1.514 -0.009 -1.223 0.00
0.00      LIG
ATOM 22 H7 LIG 1 -2.271 -1.205 1.461 0.00
0.00      LIG
ATOM 23 H8 LIG 1 -2.205 -1.963 -0.121 0.00
0.00      LIG
ATOM 24 H9 LIG 1 1.698 0.753 -1.490 0.00
0.00      LIG
ATOM 25 H10 LIG 1 1.752 2.084 -0.364 0.00
0.00      LIG
ATOM 26 H11 LIG 1 4.072 0.508 -1.958 0.00
0.00      LIG
ATOM 27 H12 LIG 1 5.010 -0.284 -0.674 0.00
0.00      LIG
ATOM 28 F2 LIG 1 3.380 -1.290 -1.314 0.00
0.00      LIG
ATOM 29 H13 LIG 1 4.215 2.490 -0.254 0.00
0.00      LIG
ATOM 30 H14 LIG 1 4.920 1.391 0.964 0.00
0.00      LIG
ATOM 31 H15 LIG 1 3.401 2.242 1.312 0.00
0.00      LIG
ATOM 32 H16 LIG 1 -2.759 2.196 -1.599 0.00
0.00      LIG
ATOM 33 H17 LIG 1 -4.060 2.593 -0.450 0.00
0.00      LIG
ATOM 34 H18 LIG 1 -2.394 2.829 0.033 0.00
0.00      LIG
ATOM 35 H19 LIG 1 -4.088 -0.200 -1.536 0.00
0.00      LIG
ATOM 36 H20 LIG 1 -5.084 0.709 -0.393 0.00
0.00      LIG
ATOM 37 H21 LIG 1 -1.205 -3.722 1.309 0.00
0.00      LIG
ATOM 38 H22 LIG 1 -0.444 -3.563 -0.293 0.00
0.00      LIG
ATOM 39 H23 LIG 1 0.566 -3.692 1.168 0.00
0.00      LIG
ATOM 40 H24 LIG 1 -0.221 -1.609 1.886 0.00
0.00      LIG
END">
</form>
<script>
jmolSetCodebase("../jmol");
jmolApplet(200, "");
</script>
</body>
</html>
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Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge."  - Albert Einstein
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FREE OODBMS DOWNLOAD - A multidimensional database that combines
robust object and relational technologies, making it a perfect match
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-------------------------------------------------------
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FREE OODBMS DOWNLOAD - A multidimensional database that combines
robust object and relational technologies, making it a perfect match
for Java, C++,COM, XML, ODBC and JDBC. www.intersystems.com/match8
_______________________________________________
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--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 
55057
mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr


-------------------------------------------------------
This SF.Net email is sponsored by: InterSystems CACHE
FREE OODBMS DOWNLOAD - A multidimensional database that combines
robust object and relational technologies, making it a perfect match
for Java, C++,COM, XML, ODBC and JDBC. www.intersystems.com/match8
_______________________________________________
Jmol-users mailing list
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Re: [Jmol-users] loading a string from my database in the JmolApplet

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